wrapping problem

From: Buddhadev Maiti (chebm_at_langate.gsu.edu)
Date: Mon Nov 29 2010 - 13:41:38 CST

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Dear NAMD users,

I recently ran some NPT simulations on a very large system composed by different subunits.
What happens is that sometimes a part of the system comes out of the water box so that
due to the wrapping procedure, one of the subunits is reflected on the opposite side of the box.
Obviously in my following simulations I disabled the wrapping command and I also used a larger
water box. However, I don't want to waste my old work, so I was wondering if there is any
post-processing of the trajectory that I can use to fix the problem.

So far I tried to address the problem using ptraj. here is my script:

trajin file-in.dcd
trajout file-out.dcd CHARMM
center :1-9854 mass origin
image origin center

However this script does not always work. Sometimes I have to use an alternative script:

trajin file-in.dcd
trajout file-out.dcd CHARMM
center :1-9854 mass origin

Unfortunately, there are situations when neither of these scripts work.
The simulations I am tryiong to analyze have all been performed in the
same way, so there is no general rule that I could figure out as to when
one script is more suitable than the other. Can anyone help me ?
Is there any reliable post-processing strategy to correct the wrapping problems ?

Thanks for your help,

Maiti

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